Biology subjects

Lepretre, M.

Publications and source records attributed to Lepretre, M..

5 recordsLinked to original sources

bioRxiv2025

Two closed systems for long-term propagation of the marine tunicate Botryllus schlosseri isolated from natural seawater

Advanced methodologies for Botryllus schlosseri artificial seawater systems are needed to decrease dependency of large-scale culture on natural seawater and expand use of this important new model organism to more inland laboratories. We constructed two botryllid tunicate customized closed aquaculture systems, a static system consisting of lightly aerated jars fed with commercial filter feeder diet, and a recirculating aquaculture system (RAS) consisting of standard marine RAS components fed live microalgae and zooplankton diets. Initially, static tunicate culture yielded exponential growth in contrast to the RAS system, which yielded poor survival and negligible growth. Modifications were made to the RAS system to improve water treatment proficiency that greatly improved tunicate survival and growth. Experiments were performed isolating feed and water type as variables that differed between the static and RAS systems to evaluate their effects. A live feed combination achieved five-fold greater growth relative to a commercial concentrate diet. B. schlosseri maintained in optimized RAS water achieved two-fold faster growth relative to animals maintained with freshly prepared artificial seawater indicating that the RAS water was beneficial to the animals. Feeding frequency of the RAS system was increased from three times per week to daily. The RAS system and procedural modifications resulted in comparable growth rates in the static and RAS systems. Both optimized systems are suitable for long-term propagation and sustenance of botryllid tunicate populations supporting both sexual and asexual modes of reproduction with a current residence time of over 24 months.

zoology↗

bioRxiv2025

Proteome Dynamics Across the Blastogenic Cycle of Botryllus schlosseri Reveals Targets for Cell Immortalization

The colonial tunicate Botryllus schlosseri regenerates weekly through a cyclical process in which adult zooids are replaced by a new generation of buds. While this dynamic asexual development is a hallmark of the species, its molecular regulation remains poorly understood. This study presents the first comprehensive proteomic analysis of B. schlosseri blastogenesis at the individual zooid level, using data-independent acquisition mass spectrometry to quantify protein abundance across developmental stages. The results reveal extensive proteome remodeling between proliferating buds and degenerating zooids. Co-expression analysis identified stage-specific protein modules enriched for biosynthesis and cell cycle pathways in buds, and for apoptosis, catabolism, and metabolic remodeling in zooids. A focused comparison between takeover buds and takeover zooids uncovered distinct regulatory programs controlling proliferation and senescence. Key proteins, including CDK1, CDK2, HDAC2, and PCNA, were identified as candidate regulators of cell cycle progression. These findings provide a molecular framework for understanding regeneration in a basal chordate and offer protein targets that may enable cell cycle re-entry and long-term culture of tunicate primary cells. Summary StatementThis study maps proteome dynamics during the blastogenic cycle in Botryllus schlosseri, identifying candidate proteins that regulate cell proliferation and offer targets for tunicate cell line development.

developmental biology↗

bioRxiv2025

Copper-Induced Stress and Recovery Impacts on Organismal Phenotypes and the Underlying Proteomic Signatures in Botryllus schlosseri

This study establishes the copper tolerance range of the colonial marine tunicate Botryllus schlosseri. Furthermore, quantitative organismal phenotyping and quantitative proteomics were combined to characterize the B. schlosseri response to, and recovery from, acute copper exposure stress. Changes in the area of B. schlosseri colony systems and pigmentation provided sensitive, dose-dependent markers of exposure to, and recovery from, copper stress. Comprehensive quantitative proteomics using consistent data-independent acquisition (DIA) assay libraries revealed activation of detoxification, oxidative stress, and immune pathways during exposure to copper stress. In addition, quantitative proteomics uncovered enrichment of tissue remodeling and proliferative signaling pathways during recovery from copper stress. We identified 35 proteins whose expression closely mirrored phenotypic changes observed at the colonial system level. This specific proteome signature represents a comprehensive molecular underpinning of the organismal response of B. schlosseri to copper stress. In conclusion, this study establishes copper tolerance ranges of the invasive colonial tunicate B. schlosseri and explains the molecular underpinnings of stress-induced organismal phenotypes by identifying corresponding proteome signatures and their associated functional enrichments. Moreover, identification of copper concentrations that are stressful and highly disruptive on the molecular phenotype, yet readily recoverable from, lays a critical foundation for future studies directed at stress-induced adaptation and evolutionary trajectories of marine invertebrates in changing and novel environments.

ecology↗

bioRxiv2024

Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipod Gammarus fossarum

Metabolic pathways are targets of environmental contaminants underlying a large variability of toxic effects throughout biodiversity. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In order to improve the knowledge of the metabolism of sentinel species, in this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipod Gammarus fossarum. We revisited the assembly of RNA-seq data by de novo approaches drastically reducing RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs from G. fossarum males and females to identify organ-specific metabolic profiles. The G. fossarum metabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7,630 annotated enzymes, 2,610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. Our analysis shows organ-specific metabolic profiles, such as an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis. In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.

molecular biology↗

bioRxiv2022

From genome wide SNPs to genomic islands of differentiation: the quest for species diagnostic markers in two scleractinian corals, Pocillopora and Porites

Coral reefs are of paramount importance in marine ecosystems, where they provide support for a large part of the biodiversity. Being quite sensitive to global changes, they are therefore the prime targets for biodiversity conservation policies. However, such conservation goals require accurate species identification, which are notoriously difficult to get in these highly morphologically variable organisms, rich in cryptic species. There is an acute need for easy-to-use and resolutive species diagnostic molecular markers. The present study builds on the huge sequencing effort developed during the TARA Pacific expedition to develop a genotyping strategy to assign coral samples to the correct species within two coral genera (Porites and Pocillopora). For this purpose, we developed a technique that we called "Divergent Fragment" based on the sequencing of a less than 2kb long diagnostic genomic fragment determined from the metagenomic data of a subset of the corals collected. This method has proven to be rapid, resolvable and cost-effective. Sequencing of PCR fragments nested along the species diagnostic fragment allowed us to assign 232 individuals of the genus Pocillopora and 247 individuals of the genus Porites to previously identified independent genetic lineages (i.e. species). This genotyping method will allow to fully analyze the coral samples collected across the Pacific during the Tara Pacific expedition and opens technological perspectives in the field of population genomics-guided conservation.

evolutionary biology↗